Observation and Fix: Sqlalchemy 2.0 Compatibility - Downgrade to Sqlalchemy 1.x
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- Dominant language
- Python
- Stars
- 265
- Forks
- 65
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Description
Just for information and to help other users of Biophi:
I installed Biophi using miniforge by following instructions provided on the project's github page.
However there was a runtime error:
AttributeError: 'Engine' object has no attribute 'execute'
I could track the issue down to a change in Sqlalchemy 2.0. Downgrading to Sqlalchemy via conda did the trick:
https://docs.sqlalchemy.org/en/14/changelog/migration_20.html
It is about engine.execute() which was deprecated in 1.4 and removed in 2.0.
$ conda install "sqlalchemy<2.0"
That installed sqlalchemy-1.4.46.
Kind regards and many thanks for providing Biophi, a great application!
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reproducing the runtime error from the Miniforge installation with SQLAlchemy 2.0, then locate the use of the removed Engine.execute() API. Confirm the application works with SQLAlchemy 2.0 without requiring a downgrade; the issue does not name specific files or tests.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python, sqlalchemy
- Domain
- databases
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100